how to interpret NES(normalized enrichment score)?

Question

[ghmdsr]

hi i'm first-year graduate student.

I got the result of my analysis in which NES is included.

I wonder about the meaning of positive score/negative score of NES.

I know that NES negative score means weaker relative activity in a sample compared with the background population, and positive score means greater relative activity .

I ask you that

1. if i got negative NES, that means nonrespondent have weaker relative activity than respondent group.

2. if i change first column(nonres) with second column(res),

   negative NES -> respondent group have weaker relative activity than nonrespondent group??

   In a nut shell, can i interpret the result depending on design matrix??

---

<designmatrix> 


here is my desigmatrix of my 5 samples.

nonres res
   0      1
   1      0
   1      0
   1      0
   0      1

Answer 1

[Pietro]

Maybe it's not super clear, but try to have a look at this question about GSEA

Answer 2

[johnsonnathant]

I assume the 'NES' type abbreviation is coming from the GSEA analysis that can be commonly run via R (https://bioconductor.org/packages/release/bioc/html/fgsea.html) that was made popular through the BROAD (http://software.broadinstitute.org/gsea/index.jsp). Since its not completely obvious what it stands for here is the definition:

NES = enrichment score normalized to mean enrichment of random samples of the same size

Meaning, the enrichment score given normalized based on the number of genes in the gene set, 'same size' is the key descriptor in the explanation. Hope that helps!

[sliders]

This is not correct - it's normalized to the mean enrichment of random samples of the same size. The method employs random sampling of gene sets of the same size as the gene set being tested to assess significance and for normalization. The number of samplings is specified as a parameter.